Characterization of Biologic Drugs: An Overview

Intact Mass and Subunit Fragment Analyses

Intact mass is the assessment of a protein’s molecular weight without digesting the compound into smaller subunits. Intact mass analysis provides insight into post-translational modifications, structural arrangement, stability, and overall protein structure.

Intact mass analyses are performed via LC-MS with minimal sample preparation and straightforward data interpretation. Generally, the drug substance or the drug product is diluted and injected in an LC-MS method. The results of the intact mass analysis can confirm the expected mass of the protein (ID), identify the major glycosylations, and any C- and/or N-terminal modifications.

Fragment mass analyses require additional sample preparation steps. Subunits can be prepared by the reduction of inter-chain disulfide bonds, by using enzymes to cleave a specific bond in the hinge region of a mAb, by enzymatically releasing the N-glycosylation, or any combination of these. The results of the fragment analyses can additionally identify modifications such as oxidations and glycations, as well as assign these modifications to a particular fragment. The analysis of the de N-glycosylated protein offers insight into the core biopharmaceutical structure, and often mandated by internal quality protocols.

At Emery Pharma, intact and fragment mass analyses are performed on a Thermo Scientific™ Exploris 240 UPLC-MS system with the Biopharma option that offer unprecedented mass range for intact mass analyses (m/z up to 8000).

Figure 1. Schematic representation of an intact IgG1 antibody undergoing IdeS-based cleavage and subsequent reduction for Subunit analyses.

Figure 2. LC-MS chromatogram acquired on a Vanquish UPLC system connected to an Exploris 240 Orbitrap HRMS depicting IgG1 antibody subunits.


Peptide Mapping

Peptide mapping is the digest of a protein by an enzyme, typically trypsin, into several smaller peptides which are then separated by chromatography and analyzed by either a mass spectrometer (LC-MS) or UV (LC-UV) detector. Additional proteolytic enzymes (e.g., Lys-C, Glu-C, chymotrypsin) may be considered to achieve full sequence coverage during peptide mapping studies.

LC-MS-based peptide mapping offers an in-depth understanding of the peptide sequence. This analysis can confirm the identity of the primary sequence, characterize modifications to the amino acids in the sequence such as post-translational modifications (PTMs) and glycosylations, map the disulfide bonds, and elucidate misincorporations in the amino acid sequence.

Additionally, peptide mapping may be performed via LC-UV analyses. While less specific than LC-MS, LC-UV-based peptide mapping is less expensive and can be conveniently performed at a wider number of laboratories. Such analyses are usually performed after establishing LC-MS-based peptide maps during the course of drug development, and frequently utilized as an ID test for GMP release and stability studies.

At Emery Pharma, we have extensive experience with both LC-MS and LC-UV-based peptide mapping studies, conducted on high field Orbitrap mass spectrometer

Figure 3. Schematic representation of a standardized Peptide Mapping workflow at Emery Pharma.

Figure 4. Schematic representation of an IgG1 antibody with relevant structural components labeled.

Figure 5. Graphic presentation of oligosaccharides (glycans) commonly bound to therapeutic antibodies.


Glycan Profiling

N-Glycosylation is a co-translational process that widely occurs during the expression of biologic compounds in mammalian and eukaryotic cells, but rarely in bacterial cells.  A variety of different oligosaccharides (glycans) are bound to the biologic molecule, and this is called the glycan profile.

It is important to identify the glycans throughout the development cycle of the biopharmaceutical for several reasons. The glycan profile impacts the safety and efficacy of the biologic compound, and a consistent glycan profile during development and commercialization indicates process stability.  Additionally, an immune response can be triggered by the appearance of an unrecognized glycan.  The glycan profile also reflects the health of the cells during the protein expression process.

Emery Pharma has expertise in several methodologies that characterize the variety of glycans which are bound to the biologic. The simplest protocol involves intact and fragment mass analyses, however, only the most abundant glycans are observed by this method. The definitive and most sensitive technique involves the enzymatic release of the glycans, followed by labeling of the glycans and injection into the UPLC-MS system. The identities of the glycans are confirmed by both mass spectrometry and by comparison of retention times to authentic standards.


Figure 6. Reaction mechanism for 2-aminobenzamide (2-AB)-based labeling (derivatization) of released glycans.


Host Cell Proteins (HCPs)

Host cell proteins (HCPs) are protein impurities found in the biopharmaceutical product, which are produced by the cell lines used to express the biologic drug. HCPs are characteristic of the expression system and are normally present in minor/residual amounts in the final product. HCPs in any biologic drug product need to be closely monitored as they may cause immunogenicity in individuals, reduce the potency, stability, or overall effectiveness of the biologic. HCPs are monitored throughout the development process and the method is validated prior to commercialization.

Emery Pharma characterizes the HCP impurities by utilizing modern UPLC-MS techniques and methods with a high field Orbitrap mass spectrometer during process and product development. Once the process is established, Emery Pharma has a full suite of bioanalysis tools, e.g., LC-MS/MS, ligand binding assays, ELISA, etc. to perform HCP assays.

Figure 7. Schematic representation of a standardized Peptide Mapping workflow at Emery Pharma, also generally utilized (protocol modified for low level protein ID) for accessing Host Cell Proteins (HCPs) in a Biologic drug substance/product.


Size Exclusion Chromatography (SEC), Ion Exchange Chromatography (IEX), and other HPLC Analysis of Biologics

 Size Exclusion Chromatography (SEC) and Ion Exchange Chromatography (IEX) are specialized HPLC techniques that are workhorse methods in the analysis of biologic compounds used for release and stability testing. Emery Pharma has expertise and equipment to provide analyses and interpretations of all aspects of these methods.

SEC methods are useful for assessing size variation and aggregation, while IEX methods are useful for assessing charge variants and purity. IEX methods are also frequently used for ID testing compared to an authentic standard. These methods can also be scaled up to provide semi-prep isolation and characterization of the observed components, and to verify chromatographic purity of the main component.

Additionally, reversed-phase HPLCX methods are very useful for ID testing, and potentially for stability-indicating methods.

All HPLC analyses at Emery Pharma is conducted on HPLC and UPLC systems from Thermo Scientific, Waters, and Agilent.

Emery Pharma

Emery Pharma is a full-service contract research laboratory, specializing in analytical, bioanalytical chemistry, microbiology & cell biology services, custom synthesis, and general R&D and cGMP/GLP support.